AP2A.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	AP2A.H12RSNP.0.PSM.A
Gene (human)	TFAP2A (GeneCards)
Gene synonyms (human)	AP2TF, TFAP2
Gene (mouse)	Tfap2a
Gene synonyms (mouse)	Ap2tf, Tcfap2a
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	14
Consensus	nddSCCYGRGGShv
GC content	70.96%
Information content (bits; total / per base)	12.753 / 0.911
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	996

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	10 (58)	0.888	0.96	0.763	0.916	0.823	0.889	2.504	3.052	204.427	424.921
Mouse	5 (34)	0.928	0.952	0.827	0.876	0.851	0.905	2.735	3.257	340.41	476.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 7 experiments	median	0.987	0.98	0.87	0.876	0.673	0.722
Overall, 7 experiments	best	0.998	0.996	0.996	0.994	0.994	0.99
Methyl HT-SELEX, 1 experiments	median	0.998	0.996	0.996	0.994	0.994	0.99
Methyl HT-SELEX, 1 experiments	best	0.998	0.996	0.996	0.994	0.994	0.99
Non-Methyl HT-SELEX, 6 experiments	median	0.979	0.969	0.848	0.852	0.67	0.71
Non-Methyl HT-SELEX, 6 experiments	best	0.993	0.99	0.989	0.981	0.983	0.973

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	30.804	6.94	0.378	0.188

TF superclass	Basic domains {1} (TFClass)
TF class	Basic helix-span-helix factors (bHSH) {1.3} (TFClass)
TF family	AP-2 {1.3.1} (TFClass)
TF subfamily	{1.3.1.0} (TFClass)
TFClass ID	TFClass: 1.3.1.0.1
HGNC	HGNC:11742
MGI	MGI:104671
EntrezGene (human)	GeneID:7020 (SSTAR profile)
EntrezGene (mouse)	GeneID:21418 (SSTAR profile)
UniProt ID (human)	AP2A_HUMAN
UniProt ID (mouse)	AP2A_MOUSE
UniProt AC (human)	P05549 (TFClass)
UniProt AC (mouse)	P34056 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	10 human, 5 mouse
HT-SELEX	6
Methyl-HT-SELEX	1

PCM	AP2A.H12RSNP.0.PSM.A.pcm
PWM	AP2A.H12RSNP.0.PSM.A.pwm
PFM	AP2A.H12RSNP.0.PSM.A.pfm
Alignment	AP2A.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	AP2A.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	AP2A.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	AP2A.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	AP2A.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	AP2A.H12RSNP.0.PSM.A_homer_format_0.001.txt AP2A.H12RSNP.0.PSM.A_homer_format_0.0005.txt AP2A.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	325.0	218.0	272.0	181.0
02	200.0	180.0	185.0	431.0
03	158.0	138.0	496.0	204.0
04	11.0	536.0	435.0	14.0
05	0.0	996.0	0.0	0.0
06	1.0	968.0	1.0	26.0
07	22.0	195.0	35.0	744.0
08	3.0	0.0	903.0	90.0
09	481.0	68.0	441.0	6.0
10	84.0	1.0	911.0	0.0
11	0.0	0.0	995.0	1.0
12	26.0	582.0	377.0	11.0
13	214.0	403.0	162.0	217.0
14	453.0	160.0	237.0	146.0

PFM

	A	C	G	T
01	0.326	0.219	0.273	0.182
02	0.201	0.181	0.186	0.433
03	0.159	0.139	0.498	0.205
04	0.011	0.538	0.437	0.014
05	0.0	1.0	0.0	0.0
06	0.001	0.972	0.001	0.026
07	0.022	0.196	0.035	0.747
08	0.003	0.0	0.907	0.09
09	0.483	0.068	0.443	0.006
10	0.084	0.001	0.915	0.0
11	0.0	0.0	0.999	0.001
12	0.026	0.584	0.379	0.011
13	0.215	0.405	0.163	0.218
14	0.455	0.161	0.238	0.147

PWM

	A	C	G	T
01	0.265	-0.132	0.088	-0.316
02	-0.217	-0.322	-0.295	0.546
03	-0.451	-0.585	0.686	-0.198
04	-2.981	0.763	0.555	-2.769
05	-4.979	1.381	-4.979	-4.979
06	-4.522	1.353	-4.522	-2.202
07	-2.358	-0.243	-1.921	1.09
08	-3.971	-4.979	1.283	-1.006
09	0.655	-1.28	0.569	-3.48
10	-1.073	-4.522	1.292	-4.979
11	-4.979	-4.979	1.38	-4.522
12	-2.202	0.845	0.412	-2.981
13	-0.15	0.479	-0.426	-0.137
14	0.595	-0.438	-0.049	-0.529

Standard thresholds

P-value	Threshold
0.001	3.53566
0.0005	4.77101
0.0001	7.27652